Re: [gmx-users] LINCS WARNING
Qiang Zhong wrote: Hellow : I am runing a MD of protein. Now I see some warning message on screen,I don't know how to understand it , Could somebody tell me about it? Thank you very much! First, consider what LINCS does. Then consider what could make LINCS unhappy with the correspondence between its inputs and outputs. Then consider what could cause that. Yes, MD is not meant to be easy. Mark ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] LINCS WARNING
> I am runing a MD of protein. Now I see some warning > message on screen,I don't know how to understand it , Could > somebody tell me about it? Thank you very much! It means that the bond between the two atoms listed there is moving too far in each time step. The reason for that problem can greatly vary. What it does mean is that something is wrong, either with the parameters or interactions in that region of the simulation, the settings used for running the simulation, or the structure in that region. Perform a search of the emailing list using that error message, and you will come up with a significant number of emails explaining it further, solutions etc. Such as these: http://www.gromacs.org/pipermail/gmx-users/2003-May/005335.html http://www.gromacs.org/pipermail/gmx-users/2006-March/020477.html http://www.gromacs.org/pipermail/gmx-users/2006-July/022578.html Plus many, many more. Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] LINCS WARNING
Hellow : I am runing a MD of protein. Now I see some warning message on screen,I don't know how to understand it , Could somebody tell me about it? Thank you very much! bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931932 33.00.1001 0.1000 0.1000 Step 1535921, time 3071.84 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001443 (between atoms 931 and 932) rms 0.50 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931934 30.50.1001 0.1000 0.1000 Step 1535922, time 3071.84 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001952 (between atoms 931 and 933) rms 0.62 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931934 35.20.1000 0.1000 0.1000 Step 1535923, time 3071.85 (ps) LINCS WARNING relative constraint deviation after LINCS: max 0.001902 (between atoms 931 and 933) rms 0.60 bonds that rotated more than 30 degrees: atom 1 atom 2 angle previous, current, constraint length 931934 33.40.1000 0.0999 0.1000 .. What happen with it,Is this harm to my result? -- Qiang Zhong Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education College of Animal Sciences and Technology Huazhong Agricultural University Wuhan,Hubei, 430070 PR China ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
RE: [gmx-users] Atoms in the .top ......
> I could figure out the problem and be able to solve it. The > problem araised because of the mix-up of the force-field files. Can you may be elaborate further so that the actual cause and solution is available in the future for people searching the archive? Catch ya, Dr. Dallas Warren Lecturer Department of Pharmaceutical Biology and Pharmacology Victorian College of Pharmacy, Monash University 381 Royal Parade, Parkville VIC 3010 [EMAIL PROTECTED] +61 3 9903 9524 - When the only tool you own is a hammer, every problem begins to resemble a nail. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
[gmx-users] Bug fixed in Gromacs-CPMD qmmm interface
Hello Gromacs-CPMD qmmm users:I found some compiler/hardware senitive bugs in the Gromacs-CPMD qmmm interface release gmx-3.3.1_qmmm-1.3 and fixed them. It has now solved the problem reported by Gireesh M Krishnan few days back and isworking fine in AMD x86-64, with GNU/Linux 2.6.9.I am waiting for further test results currently conducted by Christian Seifart in some other systems to put up this new version gmx-3.3.1_qmmm-1.3.1in our qmmm site: http://comppsi.csuohio.edu/groups/qmmm.html**As of now, THIS NEW VERSION IS AVAILABLE AT:http://comppsi.csuohio.edu/groups/people/biswas.htmlYou are encouraged to use this new version and report us, if there is any problem.cheers,pb. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi, On Feb 13, 2007, at 9:45 PM, Jones de Andrade wrote: Hi David. Ops, you are right. I missexplained, that is what I meant in the question. Well, rewriting it to have the proper and correct question: Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce "independently" the 1 - 4 LJ potentials by a factor of 0.5, and 1 - 4 coulombic interations by a factor of 0.8333, correct? Yes, but I'll nitpick since this can be important: the fudge factors specify the fraction of the interaction _remaining_ rather than the "reduction factor", so 0.8 means that it is 83% of the standard Lennard-Jones interaction. I'm sure this is what you mean since your factors are smaller than unity :-) Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Jones de Andrade wrote: Hi David. Ops, you are right. I missexplained, that is what I meant in the question. Well, rewriting it to have the proper and correct question: Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce "independently" the 1 - 4 LJ potentials by a factor of 0.5, and 1 - 4 coulombic interations by a factor of 0.8333, correct? Tnaks a lot in advance, yes. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi David. Ops, you are right. I missexplained, that is what I meant in the question. Well, rewriting it to have the proper and correct question: Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce "independently" the 1 - 4 LJ potentials by a factor of 0.5, and 1 - 4 coulombic interations by a factor of 0.8333, correct? Tnaks a lot in advance, Sincerally yours, Jones On 2/13/07, David van der Spoel <[EMAIL PROTECTED]> wrote: Jones de Andrade wrote: > Hi Erik. > > Well, I don't even use the [pairtypes] section in my files. Only use > the [pairs] one, in the way explained before. This means, so, that it > should not have any problem, and reduce "independently" the LJ > potentials by a factor of 0.5, and coulombic interations by a factor > of 0.8333, correct? > > Thanks a lot for all the help. And hope these "files structure" > examples helps someone else in the future. > > Thanks a lot. > Of course this only works for the 1-4 interactions, not the normal LJ and Coulomb interactions. Please see discussion in the manual, chapter 4. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Jones de Andrade wrote: Hi Erik. Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce "independently" the LJ potentials by a factor of 0.5, and coulombic interations by a factor of 0.8333, correct? Thanks a lot for all the help. And hope these "files structure" examples helps someone else in the future. Thanks a lot. Of course this only works for the 1-4 interactions, not the normal LJ and Coulomb interactions. Please see discussion in the manual, chapter 4. -- David. David van der Spoel, PhD, Assoc. Prof., Molecular Biophysics group, Dept. of Cell and Molecular Biology, Uppsala University. Husargatan 3, Box 596, 75124 Uppsala, Sweden phone: 46 18 471 4205 fax: 46 18 511 755 [EMAIL PROTECTED] [EMAIL PROTECTED] http://folding.bmc.uu.se ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi Erik. Well, I don't even use the [pairtypes] section in my files. Only use the [pairs] one, in the way explained before. This means, so, that it should not have any problem, and reduce "independently" the LJ potentials by a factor of 0.5, and coulombic interations by a factor of 0.8333, correct? Thanks a lot for all the help. And hope these "files structure" examples helps someone else in the future. Thanks a lot. Jones On 2/13/07, Erik Lindahl <[EMAIL PROTECTED]> wrote: Hi, That should be fine, as long as your [pairtypes] section is empty (i.e., nothing that overrides your generated values). Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi, On Feb 13, 2007, at 8:31 PM, Jones de Andrade wrote: 1 - In a top file, have the lines like this: [ defaults ] ; nbfunc com-rulegen-pairs fudgeLJ fudgeQ 12 yes 0.5000 0.8333 #include "ff_moleculeA.itp" #include "moleculeA.itp" [ system ] Pure A [ molecules ] ;molecule name nr. moleculeA 256 2 - In the ff_moleculeA.itp file, it has the [atomtypes], [bondtypes], [angletypes] and [dihedraltypes] directives, in the standard way and with all potential parameters. 3 - In the moleculeA.itp file, I included: [ moleculetype ] ; Name nrexcl moleculeA3 [atoms] directive, with atomic masses and charges included; [bonds], [angles] and [dihedrals] directives, *without* the potential parameters, just the atom indexes; And the [pairs] directive, with the "funct" included but *no* sigma or epsilon parameters. The following as an example: [ pairs ] ; aial funct sigma (nm) epsilon (kJ/mol) 9 5 1 10 5 1 11 5 1 ... Now, the question is: is it right, in a way that will use both the different valued fudgeLJ of 0.5, and the fudgeQQ of 0.8333 for 1-4 interactions, or should I make any kind of correction still? Thanks a lot in advance for everything, That should be fine, as long as your [pairtypes] section is empty (i.e., nothing that overrides your generated values). Cheers, Erik ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Atoms in the .top ......
Dear Tsjerk, I could figure out the problem and be able to solve it. The problem araised because of the mix-up of the force-field files. Thanks, Vissu. On 2/13/07, Tsjerk Wassenaar <[EMAIL PROTECTED]> wrote: Hi Viswanadham, Please explain how or where you obtained your .top and what you possibly did to it. Did you modify it? Cheers, Tsjerk On 2/13/07, Viswanadham Sridhara <[EMAIL PROTECTED]> wrote: > Hello all, > > when I run grompp, I am getting Fatal Error : Atoms in the .top are > not numbered consecutively. > > I checked the archives, this question was asked before, but I did not > find a solution or a thread email to circumvent the problem. > > I am unable to understand where this problem is coming from, I checked > .top, .gro files and they look fine, atleast to me. > > Looking forward to your response. > > Best Regards, > Viswanadham > > -- > Viswanadham Sridhara, > Research Assistant, > Old Dominion University, > Norfolk, Va-23529. > ___ > gmx-users mailing listgmx-users@gromacs.org > http://www.gromacs.org/mailman/listinfo/gmx-users > Please don't post (un)subscribe requests to the list. Use the > www interface or send it to [EMAIL PROTECTED] > Can't post? Read http://www.gromacs.org/mailing_lists/users.php > -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: [gmx-users] Atoms in the .top ......
Hi Viswanadham, Please explain how or where you obtained your .top and what you possibly did to it. Did you modify it? Cheers, Tsjerk On 2/13/07, Viswanadham Sridhara <[EMAIL PROTECTED]> wrote: Hello all, when I run grompp, I am getting Fatal Error : Atoms in the .top are not numbered consecutively. I checked the archives, this question was asked before, but I did not find a solution or a thread email to circumvent the problem. I am unable to understand where this problem is coming from, I checked .top, .gro files and they look fine, atleast to me. Looking forward to your response. Best Regards, Viswanadham -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php -- Tsjerk A. Wassenaar, Ph.D. Junior UD (post-doc) Biomolecular NMR, Bijvoet Center Utrecht University Padualaan 8 3584 CH Utrecht The Netherlands P: +31-30-2539931 F: +31-30-2537623 ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
Re: FudgeLJ in ffamber - Was: [gmx-users] Re: fudgeQQ (again ...)
Hi Erik.
Well, first of all thanks a lot for the reply. I hope I do not take
too much time from you or space on the list with this discussion.
I would like to exemplify it, and see if I'm doing it right, or where
there is a mistake. In the worst scenario, there will be an example
for anyone with the same doubt recorded forever in the list.
What I'm doing is:
1 - In a top file, have the lines like this:
[ defaults ]
; nbfunc com-rulegen-pairs fudgeLJ fudgeQ
12 yes 0.5000 0.8333
#include "ff_moleculeA.itp"
#include "moleculeA.itp"
[ system ]
Pure A
[ molecules ]
;molecule name nr.
moleculeA 256
2 - In the ff_moleculeA.itp file, it has the [atomtypes], [bondtypes],
[angletypes] and [dihedraltypes] directives, in the standard way and
with all potential parameters.
3 - In the moleculeA.itp file, I included:
[ moleculetype ]
; Name nrexcl
moleculeA3
[atoms] directive, with atomic masses and charges included;
[bonds], [angles] and [dihedrals] directives, *without* the potential
parameters, just the atom indexes;
And the [pairs] directive, with the "funct" included but *no* sigma or
epsilon parameters. The following as an example:
[ pairs ]
; aial funct sigma (nm) epsilon (kJ/mol)
9 5 1
10 5 1
11 5 1
...
Now, the question is: is it right, in a way that will use both the
different valued fudgeLJ of 0.5, and the fudgeQQ of 0.8333 for 1-4
interactions, or should I make any kind of correction still?
Thanks a lot in advance for everything,
Sincerally yours,
Jones
On 2/13/07, Erik Lindahl <[EMAIL PROTECTED]> wrote:
Hi,
On Feb 13, 2007, at 6:52 AM, Jones de Andrade wrote:
> Hi guys.
>
> Well, I'm not "exactly" trying t reopen an old discussion. I'm
> trying to see a different aspect from it, as the subject indicates.
>
> Since the message reproduced below is the last of the "fudges"
> questions, I'm worried about the fact of the fudgeLJ meaning
> nothing for the simulation.
>
> First, is it true, and there is no way around to get a working
> fudge LJ of 0.5 AND a fudgeQQ of 0.8333 in gromacs simulations?
>
No, you can certainly use fudge factors with Gromacs.
Essentially:
1. If you do not generate 1,4 ("pair") interactions they will be zero
unless you specify them explicitly.
2. If you do generate them, standard combination rules of the force
field will be applied, combined with the fudge factor.
3. If you generate pairs and still specify some interactions, those
will override the generated values.
Cheers,
Erik
___
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[gmx-users] Atoms in the .top ......
Hello all, when I run grompp, I am getting Fatal Error : Atoms in the .top are not numbered consecutively. I checked the archives, this question was asked before, but I did not find a solution or a thread email to circumvent the problem. I am unable to understand where this problem is coming from, I checked .top, .gro files and they look fine, atleast to me. Looking forward to your response. Best Regards, Viswanadham -- Viswanadham Sridhara, Research Assistant, Old Dominion University, Norfolk, Va-23529. ___ gmx-users mailing listgmx-users@gromacs.org http://www.gromacs.org/mailman/listinfo/gmx-users Please don't post (un)subscribe requests to the list. Use the www interface or send it to [EMAIL PROTECTED] Can't post? Read http://www.gromacs.org/mailing_lists/users.php
